| twinarg |
| ID: | 1384787493 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 325 (321) | ||
| Sequences: | 706 (526) | ||
| Seq/Len: | 2.199 | ||
| Nf(neff/√len): | 29.4 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 2.199).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 263_S | 266_K | 3.792 | 1.00 |
| 193_R | 227_E | 3.681 | 1.00 |
| 179_C | 233_S | 3.310 | 1.00 |
| 26_A | 86_V | 3.184 | 1.00 |
| 190_R | 234_R | 2.758 | 1.00 |
| 262_I | 266_K | 2.493 | 1.00 |
| 18_K | 22_N | 2.397 | 1.00 |
| 22_N | 86_V | 2.388 | 1.00 |
| 226_F | 230_V | 2.279 | 1.00 |
| 201_F | 219_A | 2.242 | 1.00 |
| 20_L | 24_I | 2.166 | 1.00 |
| 23_C | 87_I | 2.136 | 1.00 |
| 267_L | 273_L | 2.132 | 1.00 |
| 15_E | 19_R | 2.092 | 0.99 |
| 272_A | 275_V | 2.052 | 0.99 |
| 31_F | 79_S | 2.015 | 0.99 |
| 198_V | 274_V | 1.990 | 0.99 |
| 274_V | 280_T | 1.932 | 0.99 |
| 201_F | 215_Q | 1.932 | 0.99 |
| 283_L | 287_G | 1.815 | 0.98 |
| 61_A | 67_P | 1.737 | 0.97 |
| 260_G | 265_T | 1.677 | 0.96 |
| 260_G | 267_L | 1.671 | 0.96 |
| 30_I | 79_S | 1.664 | 0.96 |
| 197_L | 223_Y | 1.663 | 0.96 |
| 21_L | 25_I | 1.632 | 0.96 |
| 70_T | 74_L | 1.631 | 0.96 |
| 287_G | 293_A | 1.627 | 0.96 |
| 64_V | 134_F | 1.618 | 0.95 |
| 19_R | 90_Q | 1.618 | 0.95 |
| 210_P | 215_Q | 1.618 | 0.95 |
| 212_V | 215_Q | 1.612 | 0.95 |
| 262_I | 267_L | 1.611 | 0.95 |
| 186_P | 233_S | 1.594 | 0.95 |
| 280_T | 289_D | 1.593 | 0.95 |
| 287_G | 296_G | 1.590 | 0.95 |
| 19_R | 93_A | 1.581 | 0.95 |
| 89_Y | 93_A | 1.556 | 0.94 |
| 196_V | 226_F | 1.546 | 0.94 |
| 295_K | 303_D | 1.516 | 0.93 |
| 280_T | 287_G | 1.512 | 0.93 |
| 79_S | 83_S | 1.501 | 0.92 |
| 130_F | 134_F | 1.466 | 0.91 |
| 187_E | 191_K | 1.464 | 0.91 |
| 47_A | 51_K | 1.461 | 0.91 |
| 263_S | 267_L | 1.428 | 0.90 |
| 26_A | 83_S | 1.422 | 0.89 |
| 175_I | 189_L | 1.415 | 0.89 |
| 277_L | 280_T | 1.410 | 0.89 |
| 303_D | 306_A | 1.407 | 0.89 |
| 111_L | 115_S | 1.398 | 0.88 |
| 123_A | 127_F | 1.385 | 0.88 |
| 261_E | 266_K | 1.382 | 0.88 |
| 19_R | 98_A | 1.374 | 0.87 |
| 66_S | 150_D | 1.373 | 0.87 |
| 288_G | 296_G | 1.366 | 0.87 |
| 186_P | 237_V | 1.358 | 0.86 |
| 23_C | 26_A | 1.355 | 0.86 |
| 187_E | 190_R | 1.337 | 0.85 |
| 61_A | 145_V | 1.331 | 0.85 |
| 260_G | 266_K | 1.320 | 0.84 |
| 275_V | 280_T | 1.319 | 0.84 |
| 193_R | 197_L | 1.313 | 0.84 |
| 59_M | 75_T | 1.309 | 0.84 |
| 180_W | 236_Y | 1.304 | 0.83 |
| 27_V | 83_S | 1.303 | 0.83 |
| 261_E | 267_L | 1.302 | 0.83 |
| 22_N | 90_Q | 1.302 | 0.83 |
| 179_C | 186_P | 1.300 | 0.83 |
| 304_D | 307_A | 1.297 | 0.83 |
| 65_A | 137_L | 1.295 | 0.83 |
| 283_L | 293_A | 1.282 | 0.82 |
| 188_D | 192_K | 1.282 | 0.82 |
| 260_G | 264_I | 1.270 | 0.81 |
| 178_L | 183_I | 1.265 | 0.81 |
| 84_A | 111_L | 1.264 | 0.80 |
| 107_V | 115_S | 1.262 | 0.80 |
| 171_V | 200_A | 1.258 | 0.80 |
| 194_P | 215_Q | 1.250 | 0.79 |
| 8_P | 11_T | 1.242 | 0.79 |
| 266_K | 269_V | 1.233 | 0.78 |
| 190_R | 193_R | 1.232 | 0.78 |
| 98_A | 302_N | 1.230 | 0.78 |
| 190_R | 227_E | 1.229 | 0.78 |
| 7_Q | 74_L | 1.227 | 0.78 |
| 7_Q | 11_T | 1.225 | 0.78 |
| 283_L | 300_A | 1.222 | 0.77 |
| 281_K | 285_T | 1.214 | 0.77 |
| 62_T | 150_D | 1.210 | 0.76 |
| 266_K | 273_L | 1.209 | 0.76 |
| 111_L | 302_N | 1.198 | 0.75 |
| 145_V | 151_I | 1.183 | 0.74 |
| 287_G | 291_G | 1.180 | 0.74 |
| 167_V | 242_N | 1.180 | 0.74 |
| 215_Q | 219_A | 1.167 | 0.73 |
| 27_V | 76_F | 1.166 | 0.72 |
| 194_P | 277_L | 1.165 | 0.72 |
| 1_M | 4_E | 1.162 | 0.72 |
| 192_K | 196_V | 1.148 | 0.71 |
| 268_L | 272_A | 1.137 | 0.70 |
| 119_Y | 123_A | 1.135 | 0.70 |
| 27_V | 79_S | 1.128 | 0.69 |
| 83_S | 87_I | 1.125 | 0.69 |
| 195_Y | 199_G | 1.122 | 0.68 |
| 128_V | 217_L | 1.120 | 0.68 |
| 260_G | 273_L | 1.120 | 0.68 |
| 41_I | 78_V | 1.120 | 0.68 |
| 270_V | 277_L | 1.119 | 0.68 |
| 184_T | 189_L | 1.117 | 0.68 |
| 287_G | 300_A | 1.114 | 0.67 |
| 61_A | 151_I | 1.108 | 0.67 |
| 264_I | 267_L | 1.104 | 0.66 |
| 289_D | 293_A | 1.104 | 0.66 |
| 284_R | 292_A | 1.092 | 0.65 |
| 96_A | 100_Y | 1.090 | 0.65 |
| 276_L | 286_L | 1.090 | 0.65 |
| 200_A | 204_G | 1.090 | 0.65 |
| 192_K | 195_Y | 1.088 | 0.65 |
| 61_A | 66_S | 1.085 | 0.64 |
| 113_S | 173_V | 1.083 | 0.64 |
| 33_C | 71_P | 1.081 | 0.64 |
| 294_I | 304_D | 1.079 | 0.64 |
| 9_L | 18_K | 1.078 | 0.64 |
| 261_E | 273_L | 1.076 | 0.64 |
| 229_G | 275_V | 1.075 | 0.63 |
| 141_A | 147_V | 1.066 | 0.62 |
| 207_L | 218_L | 1.063 | 0.62 |
| 189_L | 214_S | 1.056 | 0.61 |
| 176_V | 236_Y | 1.055 | 0.61 |
| 227_E | 231_F | 1.054 | 0.61 |
| 280_T | 284_R | 1.050 | 0.61 |
| 99_L | 103_E | 1.048 | 0.61 |
| 184_T | 273_L | 1.046 | 0.60 |
| 95_I | 300_A | 1.041 | 0.60 |
| 317_Q | 322_S | 1.040 | 0.60 |
| 197_L | 201_F | 1.039 | 0.60 |
| 260_G | 269_V | 1.038 | 0.59 |
| 186_P | 190_R | 1.037 | 0.59 |
| 196_V | 200_A | 1.031 | 0.59 |
| 21_L | 134_F | 1.030 | 0.59 |
| 44_L | 127_F | 1.026 | 0.58 |
| 165_F | 210_P | 1.023 | 0.58 |
| 181_M | 184_T | 1.019 | 0.57 |
| 138_A | 147_V | 1.017 | 0.57 |
| 139_N | 171_V | 1.014 | 0.57 |
| 75_T | 123_A | 1.011 | 0.56 |
| 205_M | 212_V | 1.006 | 0.56 |
| 23_C | 98_A | 1.004 | 0.56 |
| 109_P | 173_V | 1.003 | 0.55 |
| 132_L | 217_L | 1.000 | 0.55 |
| 283_L | 286_L | 1.000 | 0.55 |
| 60_I | 148_S | 1.000 | 0.55 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4httA | 2 | 0.6862 | 100 | 0.336 | Contact Map |
| 4b4aA | 1 | 0.6862 | 100 | 0.338 | Contact Map |
| 2l16A | 1 | 0.16 | 99.6 | 0.834 | Contact Map |
| 2lzrA | 1 | 0.1477 | 99.5 | 0.847 | Contact Map |
| 2m7xA | 1 | 0.0923 | 12.6 | 0.973 | Contact Map |
| 2l0eA | 1 | 0.0954 | 6.2 | 0.976 | Contact Map |
| 3ne5A | 1 | 0.2431 | 5.4 | 0.977 | Contact Map |
| 1sv0A | 2 | 0.0708 | 4.4 | 0.978 | Contact Map |
| 2oqkA | 1 | 0.0585 | 4.1 | 0.978 | Contact Map |
| 4m64A | 4 | 0.7077 | 2.8 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)